HRC

histidine rich calcium binding protein

Basic information

Region (hg38): 19:49151198-49155396

Links

ENSG00000130528 ∙ NCBI:3270 ∙ OMIM:142705 ∙ HGNC:5178 ∙ Uniprot:P23327 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HRC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HRC gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			46	7	2	55
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	12	2

Variants in HRC

This is a list of pathogenic ClinVar variants found in the HRC region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-49151304-C-G			Likely benign (Apr 19, 2018)
19-49151318-A-G		not specified	Uncertain significance (Jun 16, 2024)
19-49152044-G-C		not specified	Uncertain significance (Mar 16, 2022)
19-49152333-C-G		not specified	Uncertain significance (Feb 22, 2023)
19-49153289-G-C		not specified	Uncertain significance (Oct 13, 2021)
19-49153314-C-G		not specified	Uncertain significance (Aug 11, 2024)
19-49153316-T-C		not specified	Uncertain significance (Sep 14, 2022)
19-49153419-C-T		not specified	Uncertain significance (Feb 26, 2024)
19-49153431-C-T			Benign (Jun 26, 2018)
19-49153516-C-G		not specified	Uncertain significance (Nov 25, 2024)
19-49153543-G-T		not specified	Uncertain significance (Jun 03, 2024)
19-49153550-C-T		not specified	Uncertain significance (Sep 27, 2021)
19-49153605-C-G		not specified	Uncertain significance (Feb 03, 2025)
19-49153671-C-T		not specified	Uncertain significance (Dec 13, 2023)
19-49153698-G-A		not specified	Uncertain significance (Jul 09, 2024)
19-49153698-G-C		not specified	Uncertain significance (Nov 27, 2023)
19-49153705-A-C		not specified	Uncertain significance (Mar 15, 2024)
19-49153706-T-C		not specified	Uncertain significance (Nov 09, 2021)
19-49153757-G-T		not specified	Uncertain significance (May 11, 2022)
19-49153761-C-T		not specified	Likely benign (Sep 14, 2022)
19-49153764-G-T		not specified	Uncertain significance (Aug 07, 2024)
19-49153818-T-C		not specified	Uncertain significance (Oct 03, 2022)
19-49153940-T-A		not specified	Uncertain significance (Mar 01, 2023)
19-49154028-C-T		not specified	Uncertain significance (Nov 08, 2022)
19-49154071-G-C		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HRC	protein_coding	protein_coding	ENST00000252825	6	4227

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.94e-9	0.922	125494	1	253	125748	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0663	388	384	1.01	0.0000194	4737
Missense in Polyphen		63	82.637	0.76237		1108
Synonymous	-0.458	158	151	1.05	0.00000849	1152
Loss of Function	1.85	17	27.5	0.619	0.00000154	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0112	0.00716
Ashkenazi Jewish	0.00	0.00
East Asian	0.00196	0.00196
Finnish	0.00	0.00
European (Non-Finnish)	0.000326	0.000308
Middle Eastern	0.00196	0.00196
South Asian	0.00144	0.00137
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the regulation of calcium sequestration or release in the SR of skeletal and cardiac muscle.
• Pathway: Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.957
• rvis_EVS: 1.89
• rvis_percentile_EVS: 97.32

Haploinsufficiency Scores

• pHI: 0.0908
• hipred: N
• hipred_score: 0.173
• ghis: 0.388

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hrc
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype

Gene ontology

• Biological process: regulation of heart rate;muscle contraction;positive regulation of heart rate;regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum;regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion;regulation of peptidyl-serine phosphorylation;post-translational protein modification;cellular protein metabolic process;positive regulation of heart contraction;regulation of cytosolic calcium ion concentration;regulation of ryanodine-sensitive calcium-release channel activity;regulation of cell communication by electrical coupling involved in cardiac conduction;positive regulation of relaxation of cardiac muscle;regulation of calcium ion transmembrane transport
• Cellular component: endoplasmic reticulum lumen;Z disc;sarcoplasmic reticulum membrane;sarcoplasmic reticulum lumen
• Molecular function: calcium ion binding;protein binding;ion channel binding;ATPase binding